Split out of #301, which added NITROGEN_FIXING_SYMBIONT and fixed the one record it named. This is the rest of the population, which turned out to be larger than that issue suggested.
What the survey found
Sweeping kb/communities/ for rhizobial genera (Bradyrhizobium, Rhizobium, Sinorhizobium, Mesorhizobium) returns 22 taxa across 15 records, carrying:
| role |
examples |
PRIMARY_PRODUCER |
Bradyrhizobium elkanii BXYD3 (Soybean_N_Fixation_sfSynCom), three Mesorhizobium sp. LjNodule* isolates (Lotus_LjSC3), Bradyrhizobium (Soybean_Chlorophyll_Selected_Biofertilizer) |
PRIMARY_DEGRADER |
Rhizobium pusense TYQ1, Rhizobium radiobacter F2, Sinorhizobium meliloti MSC1_01, three in Panzhihua_Vanadium_Titanium_Tailings |
CROSS_FEEDER |
Bradyrhizobium (mCAFEs_Brachypodium_RCC), Bradyrhizobium japonicum, Rhizobium sp. CF142 |
SYNTROPHIC_PARTNER |
Sinorhizobium sp. (MSC1_Dominant_Core), Bradyrhizobium pachyrhizi (with PRIMARY_DEGRADER) |
| none |
Bradyrhizobium PHNZY-24-6, Rhizobium sp. OAE497, Bradyrhizobium sp. OAE829, Mesorhizobium sp. TaiHu, Mesorhizobium sp. (putative nodulator) |
Several look like exactly the substitution #301 describes — PRIMARY_PRODUCER on nodule isolates is the carbon-fixation value applied to nitrogen fixation, and SYNTROPHIC_PARTNER on Sinorhizobium sp. is what #301 corrected in Legume_Rhizobia_Mars_Simulant_Symbiosis.
Why this was not swept in #301
A bulk retro-fit would be the same guessing the issue is about. Being a rhizobium does not establish that N fixation is the role that record's source reports:
Rhizobium radiobacter (formerly Agrobacterium) is not a nodulating N fixer; PRIMARY_DEGRADER there may be right.- In
Panzhihua_Vanadium_Titanium_Tailings the taxa are tailings isolates, where degradation and cross-feeding may genuinely be what was measured.
mCAFEs_Brachypodium_RCC's Bradyrhizobium as CROSS_FEEDER could be a metabolic observation rather than a symbiosis claim.
Each needs its own record read against its cited source. That is a curation pass, not a find-and-replace.
Suggested approach
Work record by record, and only assign NITROGEN_FIXING_SYMBIONT where the record's own description or evidence states nodulation or N₂ fixation — the standard #301 applied. Where the existing trophic role is also supported, both can stand: functional_role is multivalued and several taxa already carry two.
The five carrying no role are the cheapest place to start, since adding one cannot contradict an existing claim.
Split out of #301, which added
NITROGEN_FIXING_SYMBIONTand fixed the one record it named. This is the rest of the population, which turned out to be larger than that issue suggested.What the survey found
Sweeping
kb/communities/for rhizobial genera (Bradyrhizobium,Rhizobium,Sinorhizobium,Mesorhizobium) returns 22 taxa across 15 records, carrying:PRIMARY_PRODUCERBradyrhizobium elkanii BXYD3(Soybean_N_Fixation_sfSynCom), threeMesorhizobium sp. LjNodule*isolates (Lotus_LjSC3),Bradyrhizobium(Soybean_Chlorophyll_Selected_Biofertilizer)PRIMARY_DEGRADERRhizobium pusense TYQ1,Rhizobium radiobacter F2,Sinorhizobium meliloti MSC1_01, three in Panzhihua_Vanadium_Titanium_TailingsCROSS_FEEDERBradyrhizobium(mCAFEs_Brachypodium_RCC),Bradyrhizobium japonicum,Rhizobium sp. CF142SYNTROPHIC_PARTNERSinorhizobium sp.(MSC1_Dominant_Core),Bradyrhizobium pachyrhizi(with PRIMARY_DEGRADER)Bradyrhizobium PHNZY-24-6,Rhizobium sp. OAE497,Bradyrhizobium sp. OAE829,Mesorhizobium sp. TaiHu,Mesorhizobium sp. (putative nodulator)Several look like exactly the substitution #301 describes —
PRIMARY_PRODUCERon nodule isolates is the carbon-fixation value applied to nitrogen fixation, andSYNTROPHIC_PARTNERonSinorhizobium sp.is what #301 corrected inLegume_Rhizobia_Mars_Simulant_Symbiosis.Why this was not swept in #301
A bulk retro-fit would be the same guessing the issue is about. Being a rhizobium does not establish that N fixation is the role that record's source reports:
Rhizobium radiobacter(formerly Agrobacterium) is not a nodulating N fixer;PRIMARY_DEGRADERthere may be right.Panzhihua_Vanadium_Titanium_Tailingsthe taxa are tailings isolates, where degradation and cross-feeding may genuinely be what was measured.mCAFEs_Brachypodium_RCC'sBradyrhizobiumasCROSS_FEEDERcould be a metabolic observation rather than a symbiosis claim.Each needs its own record read against its cited source. That is a curation pass, not a find-and-replace.
Suggested approach
Work record by record, and only assign
NITROGEN_FIXING_SYMBIONTwhere the record's own description or evidence states nodulation or N₂ fixation — the standard #301 applied. Where the existing trophic role is also supported, both can stand:functional_roleis multivalued and several taxa already carry two.The five carrying no role are the cheapest place to start, since adding one cannot contradict an existing claim.